FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks

Massimo Natale; Alfredo Benso; Stefano Di Carlo; Elisa Ficarra

doi:10.1016/j.gpb.2014.05.002

FunMod: a Cytoscape plugin for identifying functional modules in undirected protein-protein networks

Genomics Proteomics Bioinformatics. 2014 Aug;12(4):178-86. doi: 10.1016/j.gpb.2014.05.002. Epub 2014 Aug 19.

Authors

Massimo Natale¹, Alfredo Benso², Stefano Di Carlo², Elisa Ficarra²

Affiliations

¹ Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy. Electronic address: massimo.natale@polito.it.
² Department of Control and Computer Engineering, Politecnico di Torino, Torino 10128, Italy.

Abstract

The characterization of the interacting behaviors of complex biological systems is a primary objective in protein-protein network analysis and computational biology. In this paper we present FunMod, an innovative Cytoscape version 2.8 plugin that is able to mine undirected protein-protein networks and to infer sub-networks of interacting proteins intimately correlated with relevant biological pathways. This plugin may enable the discovery of new pathways involved in diseases. In order to describe the role of each protein within the relevant biological pathways, FunMod computes and scores three topological features of the identified sub-networks. By integrating the results from biological pathway clustering and topological network analysis, FunMod proved to be useful for the data interpretation and the generation of new hypotheses in two case studies.

Keywords: Budd–Chiari syndrome; Cytoscape; Network analysis; Network modules; Pathway analysis; Systems biology.

MeSH terms

Computational Biology*
Gene Regulatory Networks*
Humans
Metabolic Networks and Pathways*
Models, Biological*
Protein Interaction Mapping / methods*
Proteins / metabolism*
Software*

Substances

Proteins